Cell Biology Python Packages

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

deepcell

Deep learning for single cell image segmentation

deepliif

DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification

deepcell-cpu

Deep learning for single cell image segmentation

cellshape

3D shape analysis using deep learning

cellsepi

Segmentation of microscopy images and data analysis pipeline with a graphical user interface, powered by Cellpose.

pyvertexmodel

3D vertex model allowing scutoids

cello-classify

CellO

actk

Automated Cell Toolkit

spheroidpy

Python Package for the Analysis of Spheroid Microcopy Data

u-segment3d

Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

u-unwrap

Map 2D cellular shapes to disk, square and rectangle representations for analysis

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

napari-pyvertexmodel

Napari plugin to run 3D vertex model

deepcelltl

Deep learning for single cell image segmentation

biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

cellpose-mcp

MCP tools for Cellpose and napari integration

cellpose-vollseg

modification of cellpose algorithm

biosimulators-rbapy

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

napari-vesicles-segmentation

A simple plugin to detect vesicles in cells images.

cellgeometry

Statistical Cell Shape Analysis

u-unwrap3d

Surface-guided computing of arbitrary 3D surfaces and volumes by bidirectional mapping to lower dimensions

optiflow

Reconstruction of flows from kymographs with optimal transport

cellpyability

Software for the automated analysis of in cellulo high-throughput drug screening